Speaker: Dr. Eva Maria Novoa, Group Leader of the Epitranscriptomics and RNA Dynamics Group at the Centre for Genomic Regulation, Barcelona, Spain
Title: Elucidation of RNA structure dynamics using second- and third-generation sequencing technologies
Meeting the speaker
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In the last decades, it has become clear that RNAs are not simple intermediary molecules between DNA and protein, but are in fact functional molecules capable of regulating central cellular processes, such as genome organization, gene expression, splicing or decay. Because RNA is a single-stranded molecule, it tends to fold back on itself, forming stable secondary and tertiary structures by internal base pairing and other interactions. Importantly, the function of RNAs can vary depending on the specific folding that the molecule. Therefore, accurate RNA structural maps can allow for better understanding of the complexity, function, and regulation of these molecules.
Dimethyl sulphate (DMS) and 2'-hydroxyl acylation and primer extension (SHAPE) reagents have traditionally been used to obtain experimental measurements of RNA structure, providing information on base-pairing and tertiary interactions of the RNA molecules. The coupling of DMS and SHAPE chemical labelling with second-generation sequencing (i.e. DMS-Seq and SHAPE-Seq) has allowed to obtain of genome-wide RNA structure maps, providing substantial information regarding the dynamics of RNA structures in a variety of cellular contexts. Here I will present our recent results on how using these technologies, we have studied and characterized the role of mRNA structure dynamics in maternal-to-zygotic transition during zebrafish embryonic development. Furthermore, I will also discuss best bioinformatics practices on how to detect DMS-probed RNA nucleotides in these datasets.
Despite the valuable information that can be obtained using these approaches, current methods using second-generation sequencing technologies to map RNA structure have the major caveat: they do not have single molecule resolution, as they do not sequence the probed RNA molecule. For example, if two different populations of RNAs with different RNA structure exist in the cell, current methods will provide an ‘ensemble’ average view of the mRNA structure of the transcripts, instead of depicting the two existing populations, thus leading to an incomplete or misleading view of the RNA structurome. To overcome these limitations, we propose to use third-generation sequencing technologies such as Oxford Nanopore Technologies, which allows to obtain reads from native full-length RNA molecules. Here I will discuss how ONT can be exploited to produce transcriptome-wide maps of RNA structure, in individual RNA molecules.